AutoCloner

Multiple sequence alignment - TraesCS4A01G358600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS4A01G358600	chr4A	100.000	4543	0	0	1	4543	631905694	631901152	0.000000e+00	8390.0
1	TraesCS4A01G358600	chr4A	86.385	1043	74	15	1845	2879	58787949	58786967	0.000000e+00	1077.0
2	TraesCS4A01G358600	chr4A	86.320	519	50	9	947	1454	58789115	58788607	3.090000e-151	545.0
3	TraesCS4A01G358600	chr5D	92.019	2719	82	36	1845	4543	537660147	537657544	0.000000e+00	3694.0
4	TraesCS4A01G358600	chr5D	92.839	1201	68	10	1847	3039	97577327	97578517	0.000000e+00	1725.0
5	TraesCS4A01G358600	chr5D	89.184	980	61	21	875	1836	537661197	537660245	0.000000e+00	1181.0
6	TraesCS4A01G358600	chr5D	84.755	879	117	11	5	869	309877256	309876381	0.000000e+00	865.0
7	TraesCS4A01G358600	chr5D	94.343	548	17	7	3058	3596	97578661	97579203	0.000000e+00	828.0
8	TraesCS4A01G358600	chr5D	88.770	561	46	9	917	1460	97576243	97576803	0.000000e+00	671.0
9	TraesCS4A01G358600	chr5D	93.902	164	9	1	4000	4163	97579768	97579930	3.510000e-61	246.0
10	TraesCS4A01G358600	chr5D	89.333	75	7	1	3606	3679	97579247	97579321	4.840000e-15	93.5
11	TraesCS4A01G358600	chr5B	91.441	2699	141	36	946	3610	678318155	678315513	0.000000e+00	3622.0
12	TraesCS4A01G358600	chr5B	92.303	1793	94	23	1847	3610	105539479	105537702	0.000000e+00	2507.0
13	TraesCS4A01G358600	chr5B	90.717	1185	68	18	1847	3011	106951596	106952758	0.000000e+00	1541.0
14	TraesCS4A01G358600	chr5B	94.413	537	19	5	4007	4543	678315013	678314488	0.000000e+00	815.0
15	TraesCS4A01G358600	chr5B	90.982	621	30	9	3081	3679	106953053	106953669	0.000000e+00	813.0
16	TraesCS4A01G358600	chr5B	90.548	529	41	3	941	1460	106950538	106951066	0.000000e+00	691.0
17	TraesCS4A01G358600	chr5B	89.866	523	44	4	947	1460	105540526	105540004	0.000000e+00	664.0
18	TraesCS4A01G358600	chr5B	83.838	396	25	10	3614	4008	678315474	678315117	1.570000e-89	340.0
19	TraesCS4A01G358600	chr5B	91.463	164	12	2	4000	4163	105537279	105537118	1.640000e-54	224.0
20	TraesCS4A01G358600	chr5B	91.818	110	7	2	4051	4160	106953968	106954075	7.870000e-33	152.0
21	TraesCS4A01G358600	chr5B	92.308	65	3	2	3934	3998	106953804	106953866	1.740000e-14	91.6
22	TraesCS4A01G358600	chr5B	97.872	47	0	1	3606	3651	105537672	105537626	3.770000e-11	80.5
23	TraesCS4A01G358600	chr5A	88.626	1521	112	30	1558	3040	106166647	106165150	0.000000e+00	1794.0
24	TraesCS4A01G358600	chr5A	95.627	869	36	2	1	867	6005998	6006866	0.000000e+00	1393.0
25	TraesCS4A01G358600	chr5A	87.571	877	101	6	1	872	643866155	643867028	0.000000e+00	1009.0
26	TraesCS4A01G358600	chr5A	91.519	566	32	9	3056	3609	106164847	106164286	0.000000e+00	765.0
27	TraesCS4A01G358600	chr5A	89.146	562	42	11	917	1460	106167401	106166841	0.000000e+00	682.0
28	TraesCS4A01G358600	chr5A	89.773	176	11	7	4007	4182	106149930	106149762	7.650000e-53	219.0
29	TraesCS4A01G358600	chr5A	86.667	75	8	2	3606	3679	106164253	106164180	1.050000e-11	82.4
30	TraesCS4A01G358600	chr7A	96.789	872	24	2	1	868	126558766	126559637	0.000000e+00	1452.0
31	TraesCS4A01G358600	chr7A	87.805	451	45	6	1234	1681	171843978	171844421	1.870000e-143	520.0
32	TraesCS4A01G358600	chr1B	95.533	873	36	3	1	872	141762800	141761930	0.000000e+00	1393.0
33	TraesCS4A01G358600	chr1B	86.073	876	115	6	1	870	590993800	590994674	0.000000e+00	935.0
34	TraesCS4A01G358600	chr2B	90.715	937	58	10	1845	2775	10727273	10728186	0.000000e+00	1221.0
35	TraesCS4A01G358600	chr2B	83.261	693	78	22	947	1622	10726156	10726827	1.810000e-168	603.0
36	TraesCS4A01G358600	chr2A	88.114	875	93	7	1	870	731245404	731246272	0.000000e+00	1029.0
37	TraesCS4A01G358600	chr1A	88.101	874	94	6	1	869	361951893	361951025	0.000000e+00	1029.0
38	TraesCS4A01G358600	chr3D	85.236	867	122	5	7	868	114221238	114220373	0.000000e+00	887.0
39	TraesCS4A01G358600	chr7D	88.889	450	42	5	1234	1681	366418209	366417766	8.590000e-152	547.0
40	TraesCS4A01G358600	chr7D	89.091	440	40	4	1234	1671	158431798	158431365	1.440000e-149	540.0
41	TraesCS4A01G358600	chrUn	87.805	451	45	6	1234	1681	220534998	220534555	1.870000e-143	520.0
42	TraesCS4A01G358600	chrUn	87.361	451	47	6	1234	1681	374993382	374993825	4.050000e-140	508.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS4A01G358600	chr4A	631901152	631905694	4542	True	8390.000000	8390	100.000000	1	4543	1	chr4A.!!$R1	4542
1	TraesCS4A01G358600	chr4A	58786967	58789115	2148	True	811.000000	1077	86.352500	947	2879	2	chr4A.!!$R2	1932
2	TraesCS4A01G358600	chr5D	537657544	537661197	3653	True	2437.500000	3694	90.601500	875	4543	2	chr5D.!!$R2	3668
3	TraesCS4A01G358600	chr5D	309876381	309877256	875	True	865.000000	865	84.755000	5	869	1	chr5D.!!$R1	864
4	TraesCS4A01G358600	chr5D	97576243	97579930	3687	False	712.700000	1725	91.837400	917	4163	5	chr5D.!!$F1	3246
5	TraesCS4A01G358600	chr5B	678314488	678318155	3667	True	1592.333333	3622	89.897333	946	4543	3	chr5B.!!$R2	3597
6	TraesCS4A01G358600	chr5B	105537118	105540526	3408	True	868.875000	2507	92.876000	947	4163	4	chr5B.!!$R1	3216
7	TraesCS4A01G358600	chr5B	106950538	106954075	3537	False	657.720000	1541	91.274600	941	4160	5	chr5B.!!$F1	3219
8	TraesCS4A01G358600	chr5A	6005998	6006866	868	False	1393.000000	1393	95.627000	1	867	1	chr5A.!!$F1	866
9	TraesCS4A01G358600	chr5A	643866155	643867028	873	False	1009.000000	1009	87.571000	1	872	1	chr5A.!!$F2	871
10	TraesCS4A01G358600	chr5A	106164180	106167401	3221	True	830.850000	1794	88.989500	917	3679	4	chr5A.!!$R2	2762
11	TraesCS4A01G358600	chr7A	126558766	126559637	871	False	1452.000000	1452	96.789000	1	868	1	chr7A.!!$F1	867
12	TraesCS4A01G358600	chr1B	141761930	141762800	870	True	1393.000000	1393	95.533000	1	872	1	chr1B.!!$R1	871
13	TraesCS4A01G358600	chr1B	590993800	590994674	874	False	935.000000	935	86.073000	1	870	1	chr1B.!!$F1	869
14	TraesCS4A01G358600	chr2B	10726156	10728186	2030	False	912.000000	1221	86.988000	947	2775	2	chr2B.!!$F1	1828
15	TraesCS4A01G358600	chr2A	731245404	731246272	868	False	1029.000000	1029	88.114000	1	870	1	chr2A.!!$F1	869
16	TraesCS4A01G358600	chr1A	361951025	361951893	868	True	1029.000000	1029	88.101000	1	869	1	chr1A.!!$R1	868
17	TraesCS4A01G358600	chr3D	114220373	114221238	865	True	887.000000	887	85.236000	7	868	1	chr3D.!!$R1	861

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
895	915	0.029989	CCCTAGTAAGCCCTCCCCTT	60.030	60.0	0.00	0.00	3.95	F
1523	1630	0.029834	GCGATACAATTGCAGCCAGG	59.970	55.0	5.05	39.53	4.45	F
1809	2217	0.321919	TGCTCTGTTCACATCAGGCC	60.322	55.0	0.00	34.15	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1919	2424	1.667236	TTCCTACAAGCATGGCATCG	58.333	50.000	0.00	0.0	3.84	R
2477	2997	2.147958	GCTGGAAACGTACAATCCACA	58.852	47.619	7.07	38.3	4.17	R
3580	4429	1.068610	CGTGATGCGGTTCCAAAACAT	60.069	47.619	0.00	37.1	2.71	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
130	131	7.576451	GTGGAACATATGCTGGCAACAACAT	62.576	44.000	1.58	0.00	46.77	2.71
363	373	3.430862	GCGATTTCACGGCCTGCA	61.431	61.111	0.00	0.00	0.00	4.41
396	406	1.679139	CACCTGCTGACCACTTCAAA	58.321	50.000	0.00	0.00	32.21	2.69
426	436	1.661509	CGCAGCTGTGTCTCGTTCA	60.662	57.895	19.30	0.00	0.00	3.18
613	630	1.675310	CTCGGATTGCAAGGTGGCA	60.675	57.895	4.94	0.00	43.19	4.92
895	915	0.029989	CCCTAGTAAGCCCTCCCCTT	60.030	60.000	0.00	0.00	0.00	3.95
896	916	1.132500	CCTAGTAAGCCCTCCCCTTG	58.868	60.000	0.00	0.00	0.00	3.61
899	919	0.992695	AGTAAGCCCTCCCCTTGTTC	59.007	55.000	0.00	0.00	0.00	3.18
900	920	0.992695	GTAAGCCCTCCCCTTGTTCT	59.007	55.000	0.00	0.00	0.00	3.01
901	921	2.193993	GTAAGCCCTCCCCTTGTTCTA	58.806	52.381	0.00	0.00	0.00	2.10
902	922	1.755200	AAGCCCTCCCCTTGTTCTAA	58.245	50.000	0.00	0.00	0.00	2.10
905	925	2.168496	GCCCTCCCCTTGTTCTAAAAC	58.832	52.381	0.00	0.00	35.85	2.43
1017	1046	1.080093	GATGGGTCGCGACAAGTCA	60.080	57.895	37.26	27.55	0.00	3.41
1105	1134	0.392863	CACCATCAAGGACATCCGCA	60.393	55.000	0.00	0.00	41.22	5.69
1153	1182	0.325671	GATGTCCCTCCTCCACCTCA	60.326	60.000	0.00	0.00	0.00	3.86
1156	1185	1.051556	GTCCCTCCTCCACCTCATCC	61.052	65.000	0.00	0.00	0.00	3.51
1206	1235	1.227823	CAACGACACAGGCAAGGGA	60.228	57.895	0.00	0.00	0.00	4.20
1207	1236	1.227853	AACGACACAGGCAAGGGAC	60.228	57.895	0.00	0.00	0.00	4.46
1217	1246	2.975536	CAAGGGACCGCCGACTTA	59.024	61.111	0.00	0.00	33.83	2.24
1220	1259	0.974010	AAGGGACCGCCGACTTATGA	60.974	55.000	0.00	0.00	33.83	2.15
1225	1264	2.104331	CGCCGACTTATGACCGCT	59.896	61.111	0.00	0.00	0.00	5.52
1226	1265	1.518572	CGCCGACTTATGACCGCTT	60.519	57.895	0.00	0.00	0.00	4.68
1258	1301	0.899717	TTTGGGCTGGTGGCTGATTC	60.900	55.000	0.00	0.00	41.46	2.52
1431	1485	1.740025	GATTCGGCTCAAAGGTGAAGG	59.260	52.381	0.00	0.00	31.88	3.46
1463	1517	1.063806	CCTGTTTCTGCTCGAGTTCG	58.936	55.000	15.13	2.88	41.45	3.95
1489	1595	5.964758	TGATTGATTGCCATGTTTTCTACC	58.035	37.500	0.00	0.00	0.00	3.18
1523	1630	0.029834	GCGATACAATTGCAGCCAGG	59.970	55.000	5.05	0.00	39.53	4.45
1586	1757	1.667724	CAGTCTGATCCATTGTTCGGC	59.332	52.381	0.00	0.00	0.00	5.54
1602	1778	1.184970	CGGCCCAATGGGTTGTTTCT	61.185	55.000	21.02	0.00	46.51	2.52
1624	1800	8.942338	TTCTGTTGGTGTATATGTGACTTATC	57.058	34.615	0.00	0.00	0.00	1.75
1674	1851	4.464244	TGTGGATTGTTTTGACAAAGGTGA	59.536	37.500	0.10	0.00	32.94	4.02
1693	1870	7.865530	AGGTGATTTTATTGGGGTTTAGTTT	57.134	32.000	0.00	0.00	0.00	2.66
1730	2111	1.375013	TCGCCGAGTAAGCAAACCC	60.375	57.895	0.00	0.00	0.00	4.11
1732	2113	0.953960	CGCCGAGTAAGCAAACCCTT	60.954	55.000	0.00	0.00	0.00	3.95
1756	2137	7.840342	TTTAGCTCTTTCTCATGAACTCATC	57.160	36.000	0.00	0.00	33.61	2.92
1775	2156	1.557371	TCATCCTTGTGGCCGTTCATA	59.443	47.619	0.00	0.00	0.00	2.15
1786	2167	4.023193	GTGGCCGTTCATATTTCCTAATGG	60.023	45.833	0.00	0.00	0.00	3.16
1809	2217	0.321919	TGCTCTGTTCACATCAGGCC	60.322	55.000	0.00	0.00	34.15	5.19
1877	2376	5.063180	TCTGCACAAAATTGATGGTCATC	57.937	39.130	0.00	4.13	38.29	2.92
1919	2424	5.176592	AGCACCTTTACGGAGTCTAAATTC	58.823	41.667	0.00	0.00	43.93	2.17
2462	2976	7.112779	TCATATCTTCACCGATCATAGAGCTA	58.887	38.462	0.00	0.00	0.00	3.32
2473	2993	5.182950	CGATCATAGAGCTAGTTCATCTGGT	59.817	44.000	9.43	0.00	0.00	4.00
2474	2994	5.781210	TCATAGAGCTAGTTCATCTGGTG	57.219	43.478	9.43	4.17	0.00	4.17
2475	2995	4.586421	TCATAGAGCTAGTTCATCTGGTGG	59.414	45.833	9.43	0.00	0.00	4.61
2476	2996	3.107402	AGAGCTAGTTCATCTGGTGGA	57.893	47.619	9.43	0.00	0.00	4.02
2477	2997	3.652055	AGAGCTAGTTCATCTGGTGGAT	58.348	45.455	9.43	0.00	34.51	3.41
2541	3061	6.935741	TTTTATTAGTGACACACTGTGCTT	57.064	33.333	9.20	0.00	45.01	3.91
2579	3099	9.434420	TGTCCTGCTATTCAAAAATTTAAATGG	57.566	29.630	0.39	0.00	0.00	3.16
2671	3191	1.134877	TCTGCAGATGCTACTGTGAGC	60.135	52.381	13.74	0.00	43.16	4.26
2927	3455	2.389059	CGCCTCTCGTATGATTCACAG	58.611	52.381	0.00	0.00	0.00	3.66
2978	3515	0.606401	CACCTGGACCGTTCTGCAAT	60.606	55.000	0.00	0.00	0.00	3.56
2990	3527	5.827797	ACCGTTCTGCAATAATAATGGTCAT	59.172	36.000	0.00	0.00	36.70	3.06
3082	3910	1.005924	GCAGGGGGAATCCTTTCTTCA	59.994	52.381	0.00	0.00	34.31	3.02
3229	4061	4.347583	TCCTTGGTTCATTTTGGCAAGATT	59.652	37.500	0.00	0.00	0.00	2.40
3232	4064	7.398618	TCCTTGGTTCATTTTGGCAAGATTATA	59.601	33.333	0.00	0.00	0.00	0.98
3263	4112	3.379688	GCCTTTCCTTCTATGGCTCTTTG	59.620	47.826	0.00	0.00	40.36	2.77
3283	4132	5.910637	TTGTGAATCTTGCTTCAAAATGC	57.089	34.783	0.00	0.00	36.92	3.56
3284	4133	5.204409	TGTGAATCTTGCTTCAAAATGCT	57.796	34.783	0.00	0.00	36.92	3.79
3285	4134	5.603596	TGTGAATCTTGCTTCAAAATGCTT	58.396	33.333	0.00	0.00	36.92	3.91
3359	4208	1.134075	GTTCATGCTGTGCGCTCTG	59.866	57.895	9.73	10.76	40.11	3.35
3403	4252	2.737180	CGTGGGACAGCTGACACT	59.263	61.111	23.35	0.00	41.80	3.55
3596	4445	3.467374	AACAATGTTTTGGAACCGCAT	57.533	38.095	0.00	0.00	37.15	4.73
3736	4622	2.087646	GTCTCCTGAGAAAACATGGGC	58.912	52.381	0.00	0.00	39.48	5.36
3814	4700	5.234116	CACATTTTGGTGTGCTTTTACTTCC	59.766	40.000	0.00	0.00	42.51	3.46
3820	4706	6.177310	TGGTGTGCTTTTACTTCCTACTTA	57.823	37.500	0.00	0.00	0.00	2.24
3845	4731	3.713764	ACTAGCCTGGAACATCTAGCAAT	59.286	43.478	0.00	0.00	41.72	3.56
3854	4740	4.569966	GGAACATCTAGCAATCTGTGACTG	59.430	45.833	0.00	0.00	0.00	3.51
3906	4793	6.816640	TGTCGAAAGGTCTATTATGAAAGGTG	59.183	38.462	0.00	0.00	0.00	4.00
3927	4814	6.492772	AGGTGATGAAAAAGAAGATGAAGCTT	59.507	34.615	0.00	0.00	0.00	3.74
3937	4824	5.068636	AGAAGATGAAGCTTGCAAGAAGAA	58.931	37.500	30.39	12.28	0.00	2.52
3938	4825	5.711036	AGAAGATGAAGCTTGCAAGAAGAAT	59.289	36.000	30.39	16.36	0.00	2.40
3939	4826	6.883217	AGAAGATGAAGCTTGCAAGAAGAATA	59.117	34.615	30.39	10.42	0.00	1.75
4005	5199	7.182817	TGCTCACCTAACACATACTATTTCT	57.817	36.000	0.00	0.00	0.00	2.52
4046	5349	3.260632	TGCTCAGCTTAGTCCAATACACA	59.739	43.478	0.00	0.00	0.00	3.72
4047	5350	3.619038	GCTCAGCTTAGTCCAATACACAC	59.381	47.826	0.00	0.00	0.00	3.82
4143	5446	8.602328	GTGAATATCATGTCAACAAGAGAAGAG	58.398	37.037	0.00	0.00	0.00	2.85
4515	5818	2.941064	TGCATGATCAGCTTAGCAGAAC	59.059	45.455	7.07	3.23	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	2.676471	AATGGCGCCAACTGTCCC	60.676	61.111	36.33	0.00	0.00	4.46
130	131	2.339418	CCATAGTCGTGCGTTTGGTTA	58.661	47.619	0.00	0.00	0.00	2.85
396	406	0.806868	CAGCTGCGTCCACATTGATT	59.193	50.000	0.00	0.00	0.00	2.57
613	630	2.173356	TCCTTCCCTGATCGCATCAATT	59.827	45.455	1.44	0.00	39.11	2.32
777	794	1.982395	CCTAGCCAGGTGTGACGGA	60.982	63.158	0.00	0.00	37.15	4.69
872	892	0.837940	GGAGGGCTTACTAGGGTTGG	59.162	60.000	0.00	0.00	0.00	3.77
873	893	0.837940	GGGAGGGCTTACTAGGGTTG	59.162	60.000	0.00	0.00	0.00	3.77
895	915	9.138596	AGGGCTTACTATTTTTGTTTTAGAACA	57.861	29.630	0.00	0.00	43.73	3.18
896	916	9.622004	GAGGGCTTACTATTTTTGTTTTAGAAC	57.378	33.333	0.00	0.00	36.29	3.01
899	919	7.363530	GGGGAGGGCTTACTATTTTTGTTTTAG	60.364	40.741	0.00	0.00	0.00	1.85
900	920	6.438108	GGGGAGGGCTTACTATTTTTGTTTTA	59.562	38.462	0.00	0.00	0.00	1.52
901	921	5.247564	GGGGAGGGCTTACTATTTTTGTTTT	59.752	40.000	0.00	0.00	0.00	2.43
902	922	4.775780	GGGGAGGGCTTACTATTTTTGTTT	59.224	41.667	0.00	0.00	0.00	2.83
905	925	2.949644	CGGGGAGGGCTTACTATTTTTG	59.050	50.000	0.00	0.00	0.00	2.44
911	931	2.445274	GGCGGGGAGGGCTTACTA	60.445	66.667	0.00	0.00	0.00	1.82
1206	1235	2.493030	CGGTCATAAGTCGGCGGT	59.507	61.111	7.21	0.00	0.00	5.68
1207	1236	2.901051	AAGCGGTCATAAGTCGGCGG	62.901	60.000	7.21	0.00	35.09	6.13
1217	1246	2.543067	GAAGCCCCTGAAGCGGTCAT	62.543	60.000	0.00	0.00	35.07	3.06
1220	1259	4.394712	CGAAGCCCCTGAAGCGGT	62.395	66.667	0.00	0.00	34.64	5.68
1225	1264	0.323360	CCCAAATCGAAGCCCCTGAA	60.323	55.000	0.00	0.00	0.00	3.02
1226	1265	1.302949	CCCAAATCGAAGCCCCTGA	59.697	57.895	0.00	0.00	0.00	3.86
1258	1301	2.046892	CCTGCGAGAACCCACCAG	60.047	66.667	0.00	0.00	0.00	4.00
1411	1465	1.740025	CCTTCACCTTTGAGCCGAATC	59.260	52.381	0.00	0.00	31.71	2.52
1431	1485	0.671796	AAACAGGGTAAGCAAACGCC	59.328	50.000	2.49	0.00	33.02	5.68
1463	1517	7.223387	GGTAGAAAACATGGCAATCAATCAATC	59.777	37.037	0.00	0.00	0.00	2.67
1523	1630	1.530323	ACAACCTAATCGCACAACCC	58.470	50.000	0.00	0.00	0.00	4.11
1624	1800	1.051812	AGGGTCCACTCAGACAAGTG	58.948	55.000	0.00	0.00	45.10	3.16
1631	1807	0.322975	CCAGAACAGGGTCCACTCAG	59.677	60.000	0.00	0.00	0.00	3.35
1674	1851	9.456147	GCCAAATAAACTAAACCCCAATAAAAT	57.544	29.630	0.00	0.00	0.00	1.82
1693	1870	3.126858	GCGACAGTGAATTCAGCCAAATA	59.873	43.478	8.80	0.00	0.00	1.40
1730	2111	7.664082	TGAGTTCATGAGAAAGAGCTAAAAG	57.336	36.000	0.00	0.00	35.08	2.27
1732	2113	7.389232	TGATGAGTTCATGAGAAAGAGCTAAA	58.611	34.615	0.00	0.00	36.57	1.85
1756	2137	2.036958	TATGAACGGCCACAAGGATG	57.963	50.000	2.24	0.00	36.89	3.51
1842	2341	5.403897	TTTGTGCAGAACTAAAGAAGTCG	57.596	39.130	0.00	0.00	37.50	4.18
1877	2376	3.679502	TGCTTGTATGATCAGTGACAACG	59.320	43.478	13.70	11.61	0.00	4.10
1919	2424	1.667236	TTCCTACAAGCATGGCATCG	58.333	50.000	0.00	0.00	0.00	3.84
2372	2886	3.793559	AGATACGGGTTACAATCTGTGC	58.206	45.455	0.00	0.00	29.82	4.57
2473	2993	3.244596	TGGAAACGTACAATCCACATCCA	60.245	43.478	7.07	0.00	38.30	3.41
2474	2994	3.340034	TGGAAACGTACAATCCACATCC	58.660	45.455	7.07	0.00	38.30	3.51
2475	2995	3.181510	GCTGGAAACGTACAATCCACATC	60.182	47.826	7.07	0.00	38.30	3.06
2476	2996	2.747446	GCTGGAAACGTACAATCCACAT	59.253	45.455	7.07	0.00	38.30	3.21
2477	2997	2.147958	GCTGGAAACGTACAATCCACA	58.852	47.619	7.07	0.00	38.30	4.17
2541	3061	2.551270	AGCAGGACACCAGGAGATAAA	58.449	47.619	0.00	0.00	0.00	1.40
2579	3099	3.428589	GCTGACCTGCCAAAAGATGAATC	60.429	47.826	0.00	0.00	0.00	2.52
2671	3191	7.283807	TCACTCATTTCATCAACATTGGGATAG	59.716	37.037	0.00	0.00	0.00	2.08
2962	3499	5.277974	CCATTATTATTGCAGAACGGTCCAG	60.278	44.000	0.00	0.00	0.00	3.86
2990	3527	8.034215	CCTACAACATCATCAGCCAAAATAAAA	58.966	33.333	0.00	0.00	0.00	1.52
3082	3910	6.014669	TGGCTGGCTTTTGAGTTAATACAATT	60.015	34.615	2.00	0.00	0.00	2.32
3133	3965	7.176515	ACATCCATGCAAACTATGTTCAGTTTA	59.823	33.333	0.00	0.00	44.86	2.01
3232	4064	6.746614	GCCATAGAAGGAAAGGCAGATAAGAT	60.747	42.308	0.00	0.00	44.59	2.40
3236	4068	4.357918	GCCATAGAAGGAAAGGCAGATA	57.642	45.455	0.00	0.00	44.59	1.98
3263	4112	5.924825	AGAAGCATTTTGAAGCAAGATTCAC	59.075	36.000	0.00	0.00	38.87	3.18
3283	4132	7.953158	TCATGTGACTTAACAGAAGAAGAAG	57.047	36.000	0.00	0.00	32.52	2.85
3284	4133	7.933577	ACATCATGTGACTTAACAGAAGAAGAA	59.066	33.333	0.00	0.00	32.52	2.52
3285	4134	7.445121	ACATCATGTGACTTAACAGAAGAAGA	58.555	34.615	0.00	0.00	32.52	2.87
3403	4252	2.394708	GAAGTGATTCTATAGCGCGCA	58.605	47.619	35.10	19.76	0.00	6.09
3580	4429	1.068610	CGTGATGCGGTTCCAAAACAT	60.069	47.619	0.00	0.00	37.10	2.71
3655	4541	8.721133	TTGAGGGTACTCTATAATATGCTCAA	57.279	34.615	0.00	0.00	44.29	3.02
3736	4622	8.113062	CAGAAATCTCTATGTTAAAAGCTCACG	58.887	37.037	0.00	0.00	0.00	4.35
3747	4633	8.109634	ACACCAAATACCAGAAATCTCTATGTT	58.890	33.333	0.00	0.00	0.00	2.71
3752	4638	6.599638	GCTAACACCAAATACCAGAAATCTCT	59.400	38.462	0.00	0.00	0.00	3.10
3814	4700	8.184304	AGATGTTCCAGGCTAGTAATAAGTAG	57.816	38.462	0.00	0.00	0.00	2.57
3820	4706	4.901849	TGCTAGATGTTCCAGGCTAGTAAT	59.098	41.667	0.00	0.00	34.32	1.89
3845	4731	1.900585	GCGCGATTTGCAGTCACAGA	61.901	55.000	12.10	0.00	46.97	3.41
3854	4740	0.594540	TAATGGCATGCGCGATTTGC	60.595	50.000	12.10	15.20	43.19	3.68
3906	4793	6.154445	TGCAAGCTTCATCTTCTTTTTCATC	58.846	36.000	0.00	0.00	0.00	2.92
4033	5332	4.141914	TGTGTGTGTGTGTGTATTGGACTA	60.142	41.667	0.00	0.00	0.00	2.59
4046	5349	1.252175	TTTTGTGCCTGTGTGTGTGT	58.748	45.000	0.00	0.00	0.00	3.72
4047	5350	2.582728	ATTTTGTGCCTGTGTGTGTG	57.417	45.000	0.00	0.00	0.00	3.82
4143	5446	2.485582	CTGCTGCTGCTGATGTGC	59.514	61.111	17.00	1.70	40.01	4.57
4315	5618	0.104487	TGAACGCGAACAACTACCCA	59.896	50.000	15.93	0.00	0.00	4.51
4515	5818	9.520204	AATCAAACAGTCAAATTCTTACACTTG	57.480	29.630	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.